Apply for an exemption, based on long standing practice (how many years has your coop been where it is???) - but its always more difficult to get a zoning exemption after you are cited than before the tickets get written.
Otherwise, the best fight is simply to get the Ordinance amended - which doesn't help in the short term.
I will observe that, at the moment, there is a resurgence of interest in backyard chicken ownership, and that the setback in your code is far out of the usual in places that permit backyard ownership. Interesting to me, the ordinance basically forces the few people who can own chickens in the village to keep them quite close to your waterway, nearing (or in) the flood plain. That's just bad policy, in my view.